1-203682799-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001684.5(ATP2B4):c.-407T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 156,190 control chromosomes in the GnomAD database, including 55,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.83 ( 53549 hom., cov: 32)
Exomes 𝑓: 0.85 ( 1491 hom. )
Consequence
ATP2B4
NM_001684.5 5_prime_UTR
NM_001684.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.07
Publications
26 publications found
Genes affected
ATP2B4 (HGNC:817): (ATPase plasma membrane Ca2+ transporting 4) The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 4. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 21 | ENST00000357681.10 | NP_001675.3 | ||
ATP2B4 | NM_001001396.3 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 22 | NP_001001396.1 | |||
ATP2B4 | NM_001365783.2 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 21 | NP_001352712.1 | |||
ATP2B4 | NM_001365784.2 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 21 | NP_001352713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 21 | 1 | NM_001684.5 | ENSP00000350310.5 | |||
ATP2B4 | ENST00000341360.7 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 22 | 1 | ENSP00000340930.2 | ||||
ATP2B4 | ENST00000705901.1 | c.-407T>C | 5_prime_UTR_variant | Exon 2 of 21 | ENSP00000516177.1 |
Frequencies
GnomAD3 genomes AF: 0.833 AC: 126602AN: 152002Hom.: 53541 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
126602
AN:
152002
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.847 AC: 3449AN: 4070Hom.: 1491 Cov.: 0 AF XY: 0.846 AC XY: 1727AN XY: 2042 show subpopulations
GnomAD4 exome
AF:
AC:
3449
AN:
4070
Hom.:
Cov.:
0
AF XY:
AC XY:
1727
AN XY:
2042
show subpopulations
African (AFR)
AF:
AC:
106
AN:
180
American (AMR)
AF:
AC:
130
AN:
154
Ashkenazi Jewish (ASJ)
AF:
AC:
140
AN:
152
East Asian (EAS)
AF:
AC:
148
AN:
148
South Asian (SAS)
AF:
AC:
141
AN:
206
European-Finnish (FIN)
AF:
AC:
92
AN:
126
Middle Eastern (MID)
AF:
AC:
8
AN:
10
European-Non Finnish (NFE)
AF:
AC:
2453
AN:
2818
Other (OTH)
AF:
AC:
231
AN:
276
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.480
Heterozygous variant carriers
0
22
45
67
90
112
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.833 AC: 126645AN: 152120Hom.: 53549 Cov.: 32 AF XY: 0.831 AC XY: 61836AN XY: 74376 show subpopulations
GnomAD4 genome
AF:
AC:
126645
AN:
152120
Hom.:
Cov.:
32
AF XY:
AC XY:
61836
AN XY:
74376
show subpopulations
African (AFR)
AF:
AC:
28225
AN:
41468
American (AMR)
AF:
AC:
13801
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
3149
AN:
3470
East Asian (EAS)
AF:
AC:
5160
AN:
5164
South Asian (SAS)
AF:
AC:
4118
AN:
4820
European-Finnish (FIN)
AF:
AC:
8704
AN:
10580
Middle Eastern (MID)
AF:
AC:
269
AN:
294
European-Non Finnish (NFE)
AF:
AC:
60546
AN:
68006
Other (OTH)
AF:
AC:
1817
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1016
2031
3047
4062
5078
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
880
1760
2640
3520
4400
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3220
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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